One year after the Black Rebellion, Lelouch Lamperouge has resumed his normal school life with no apparent memories of the year before. After skipping remedial gym class, he sets off with younger brother Rolo to gamble at Babel Tower. Led by C.C., the Order of the Black Knights launches an attack on the complex to retrieve Lelouch. C.C. reawakens Lelouch's memories, and he resumes his identity as Zero. Suzaku Kururugi declares to the Emperor that he will personally kill Zero.

Lelouch learns that the Chinese Empress Tianzi is being forced into a political marriage to First Prince Odysseus u Britannia. The wedding is orchestrated by the High Eunuchs, who will become nobility in Britannia in exchange for turning over half their land to Second Prince Schneizel el Britannia. As the wedding begins, Li Xingke initiates a coup-d'état to overthrow the Eunuchs, but before he can free the Empress, Lelouch appears and takes her hostage. Elsewhere, V.V. prepares to unleash Jeremiah Gottwald against Lelouch and C.C.

Rolo admits to causing Shirley's death; rather than blame Rolo, Lelouch blames the existence of Geass itself. In retaliation, he mounts an assault on the Geass Directorate, slaughtering every man, woman, and child within the stronghold. V.V. pilots the Siegfried in an effort to stop the Black Knights, but is defeated by both Lelouch and Cornelia. He escapes to the Thought Elevator, where Charles awaits, and when Lelouch follows he is transported to the Sword of Akasha. Meanwhile, Kallen and Nunnally discuss Lelouch. They are interupted by Suzaku, who, despite having been told that Shirley's death was a suicide, decides to interrogate Kallen using Refrain, in order to confirm his suspicion that Lelouch has become Zero again.